Chaos Users: Waves of Chaos!
by Kyuubi16
Summary: Ever since a mysterious portal ripped him from his world Naruto has been living on Mobius and helping the freedom fighters against the tyrannical mastermind Robotnik. A year has passed since a hand full of them were ripped from Mobius and sent to Earth. Robotnik's latest plan comes in the form of an ancient and angry god of destruction. Sonic Adventure focused crossover.
1. The Adventure Begins!

The Chaos Users

0

Pairings Undecided

0

''Normal Speech''

 _Inner Thoughts, Dialogue, or reading passages from books and scrolls_

(Quick Notes and Messages or Echoes.)

 **(Dark over lapping echoes)**

 **''Boss Summons, Demons, Dark beings speaking, Demonic/Angry characters Speaking as well as extremely Dark spells and Magic.''**

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Story Start

00000

A young male sat over the cliff side watching the sunset with his companion, a female cybrog rabbit. His tail nestled around her waist as they enjoyed the sincerity of there closeness. It had been a few weeks since Dr. Ivo Robotnik, a mad genius had attempted his latest plan to take over the world and build an empire, one he would christen Robotropolis.

Until he found out who opened that portal that ripped him from his world and dropped him off in Mobius and why he would be stuck here.

As such their other companion, the mad scientist's nemesis and the fast thing alive on two legs was on vacation. That beings name was Sonic The Hedgehog, a blue Anthropomorphic Hedgehog whose speeds could exceed the sound barrier. The Freedom Fighters had all met as a result of one of Robotnik's earlier schemes and since then they foiled whatever plot the madmen came up with. But for now they were enjoying the period of peace they were given knowing it was all a matter of time until Robotnik tried something else.

* * *

Up in the clouds over the Wild terrains and lush forests of the Mystic ruins was the floating island Angel Island. A large, lavish paradise that was home to ancient ruins and other terrains including winter wonderlands. In the center was the ruins of a temple that houses the legendary gem of grand power, the Master Emerald.

The bright glowing shine of the Large Green emerald pierced the dark and peaceful star filled sky. The night was beautiful as the Emerald's guardian Knuckles the Enchinda bathed in the Master's emerald dark green glow as he rested.

The stone cold floor beneath him reminded him of his duty. A duty he knew he had to do despite not knowing why. It was a strange feeling constantly haunting him. He knew nothing of his past yet felt he had to guard the emerald, as if it was programmed into his genes.

He was the last of his kind due to an unexplained incident long ago.

His extraordinary strength and affinity with the Master Emerald, together with the sign of a guardian across his chest, all pointed to his duty as the Master Emerald Guardian.

The Sacred Sky Sanctuary ruins destruction was forever engraved in his mind as a constant reminder of what could happen if the emerald's power was abused. The guardian was left to face off against the Doctor's sinister leftovers and against the power of the Master Emerald directly. The aftershock of the right left a scar on the island and the Sacred Ruins fell into the Ocean. If it wasn't for his new friends Sonic and Naruto, Knuckles would be down there with them.

Before this incident he would often leave the emerald for brief moments of time to explore the island but after that no more. He was by it's side residing in the spot that the Chaos Emeralds, gems of legendary power said to hold the power of the gods themselves were now scattered across the world due to another incident many years ago.

The Silence was then broken by the sound of Jet Engines, followed by something electrical, or some form of energy, powering up. Knuckles opened his eyes and saw nothing.

CRASH!

The floor shook beneath him as Knuckles fell onto his face. He turned around to see a strange figure in front of him.

The humanoid figure was a few inches taller then him. It's body was semi-transparent and made of water with no visible bones and organs except a small brain like object. The only human like feature or came close to it was it's eyes but those were consisted of two green orbs.

Knuckles sprang to his feet and suddenly noticed his precious Master Emerald had been shattered into pieces.

"What the? Oh no! Did you do this? Why? Answer me beast before I start throwing punches!" the guardian demanded as he dashed towards the water beast preparing a powerful punch. However as he was just about to strike the watery figure jumped up. It dropped down with mighty force knocking Knuckles a good distance from the shrine.

Knuckles raced back up to the shattered remains of the Master Emerald. Not much remained of the marvelous as just the base of the controller remained. The watery figure had completed disappeared without saying a thing. Knuckles remained as confused as ever, and as he took a moment to think about what has just happened, the main thing he was supposed to prevent happened.

 _"Oh no! Without the Master Emerald the Island will sink into the Ocean again."_

Sure enough the Island began to shake as if hit by a massive earthquake. Knuckles jumped into the air and used his glide technique to reach the end of the Floating Island without being affected by the shaking. Angel Island used the power of the Master Emerald to remain in the sky, thus hiding the most powerful of the Emeralds away from the general public.

Knuckles never questioned this, assuming it was to protect it from those who'd wish to use its power for evil. Angel Island was also his home and a sacred island to his race. He wished to preserve it best he could.

Knuckles reached the end of Angel Island and looked down towards the Ocean underneath him. To his horror the Angel Island didn't just crash into an Ocean but a huge jungle with mountains surrounding it.

Eventually a building with two giant tails settled his nerve. That had to be where Tails lived. He had to made haste to find the emerald pieces before they fell into the wrong hands.

* * *

Elsewhere in the mystic ruins area.

Buzz…..Beep

The glass of the tube disappeared and the first thing he saw was the face of his master. E-102 Gamma stepped out of the tube he had been charging in. The man in front of him gave him life and so appropriately asked for his eternal loyalty.

"Arise E-102, you are complete.''

 **"Scanning video input. File found. Subject Dr Ivo Robotnik. Master, what can I do for you?"**

"Perfect, another fine addition to my E-series. You have already identified me now identify yourself.''

 **"Scanning system….I am E-102 Gamma. 3rd in the E-series.''**

"And how are your systems? I can see your processor and database are fine. How about your cannon?"

" **All systems working at 100 percent.''**

Gamma examined the Room he was in. He found the file he needed to identify the local area. He was in the entrance room to the Final Egg base, deep within the Mystic Ruins. To his right were two more tubes. One held an unconscious Metal Sonic, probably still repairing itself after the intense race he had on Little Planet. The other held a new Robotic Sonic Prototype, equipped with machine gun hands.

"Come Gamma, it's time for you first test. Beyond this door is a little shooting gallery I've made. Try and hit all the targets.''

 **"Mission Accepted. Objective Destroy all targets.''**

Gamma ventured through the corridors of the shooting gallery section of final Egg. Lots of Dolls of the four primary targets appeared, mainly of the Foxes and the Echidna. At the end though the Hedgehog appeared, tougher than the others. The Doll moved along a rail and took three shots to break.

Gamma felt a strange sensation. Almost a feeling though that would've been impossible. He was just a robot but he felt his cannon was only adequate to do the task. That it was lacking efficiency in range, power, and sight capabilities if the rockets he produced only did the minimal damage to the latter object when it had maximal damage ratio within the specified meters against the previous objects. He still blasted into the air shouting, "Mission Complete," however and he felt a little bit of happiness too.

A machine… how could he feel these things?

Gamma decided not to dwell on it and returned to the entrance lobby. There waiting for him was Dr. Robotnik clapping his performance.

"Bravo Gamma. I think you're ready for your first real challenge already. Down there is your bigger brother E-101. Why don't you go say hello."

Gamma moved down to the lower area of the lobby where a black robot was waiting for him. It was like Gamma in every way except that instead of a hand and one laser blaster, E-101 Beta had dual missile launchers.

"Now I have a proposition for you two. I want to know who the strongest is so I'm pitting you against each other. The winner will be granted permission to join the Egg Carrier Crew as my elite task force. Personally my money is on Beta though Gamma has earned the right to at least challenge Beta.''

 **"Affirmative,"** both Robots replied at the same time.

Beta fired a barrage of missiles at Gamma though Gamma had already analyzed Beta's weakness. The missiles weren't all that fast, even if they did home into Beta's opponents they could be outrun with some speed. Gamma used that to his advantage and locked on to Beta with his laser. He then circled around Beta firing his laser and weakened Beta to his knees.

Beta fell to the ground sparking a little. Gamma fired into the air shouting "Mission Complete" again. Gamma was extremely happy with an intensity that confused him even further.

Gamma kept the emotion to himself filing it under a newly created file and calculated several ratios. He came to a 47% conclusion that it was part of an A.I. program while another 37% was filed under possible CPU errors.

The Doctor proceeded down to the arena with a big grin on his face. Gamma didn't have the strength of Beta but he managed to defeat him using Skill and tactics. Dr. Robotnik was impressed.

"Excellent Gamma. I hereby give you permission to serve aboard the Egg Carrier.''

Beta then pushed in front of Dr. Robotnik and made some beeping noises.

"What's this? You want to serve as well?''

Beta kept pushing in front of Dr. Robotnik. Annoyed the Doctor took a moment to think and then smiled.

"So you really want to come along to huh? Well Ok. I hereby grant you Special Permission to come aboard the Egg Carrier", said the Doctor, "Now, it's time for the Egg Carrier to take its place commanding the skies. Prepare the Egg Carrier for take off!"

 **"Affirmative!"** the two robots replied before disappearing into the depths on the Final Egg.

Nibi had went to sleep some time ago but Naruto couldn't get over his feelings of dread. He decided to go for a walk and went deep inside the jungle. He made his way through the forest and came across something he hadn't seen in awhile.

* * *

Meanwhile deep within the Mystic Ruins Jungle, Big the Cat lay on his bed asleep. Resting on top of his head was hid best friend. A Frog named Froggy. The peaceful night was interrupted by a loud explosion and an event was about to happen that would involve this normally neutral cat, into a fight he would normally stay out of.

Big the cat was a very large purple cat that had always lived in the Jungle. He practically raised himself and learned to fish early on in life. It became his passion, though that may be too strong a word.

It was nightfall and so the big bulky cat lay on his wooden re-enforced bed sleeping. The loud sound of a crash not all that far away wasn't enough to wake him. His little Frog friend however felt the force and fell off Big's Belly. Shaking off the pain Froggy noticed a small puddle of water that seemed to call out to him. Curious Froggy went in to investigate and then it all went black for him.

Big suddenly leapt to his feet. He felt like something bad had happened and looked down to find his frog friend had mutated noticeably. He now had a fairly large tail, in proportion to the rest of its body.

"Froggy? What happened to you buddy?'' Big asked in his deep slow talking voice.

Froggy turned with a sinister look on his face and leapt above Big in a massive jump. It landed next to a Yellow Emerald the two had found one day during fishing. To Big's surprise Froggy ate the treasure they had found.

"My Treasure! What are you doing Froggy?" The large purple feline asked Big upset.

Froggy then hopped off deep into the Jungle. Big grabbed his prized fishing Rod and went after him.

* * *

After their last big adventure Sonic went on vacation. The city was safe in Naruto and Taili's hand as the Blue Hedgehog was more interested in exploring more of this new world. Nothing pleased Sonic more than to run, and while the canyons and mountains gave him plenty of space he still wished to see more of the world. He was surprised that this world had versions similar to, Spring Yard and Casino Night cities of Mobius or maybe it was a result of that Chaos Emerald Warp thing some time ago.

The big giant Egg had gone all silent since he tricked Knuckles and tried to steal the Master Emerald to power his monstrosity, the Death Egg. Sonic had managed to destroy the evil satellite though it took him a couple of attempts. He even managed to get Angel Island back into the air. All while learning a bit of the emeralds power from Naruto.

Now though he was excited about exploring this new city, Station Square. It was a human metropolis, much larger than the ones back in Mobius.

 _"Yeah this is happening,"_ he thought out loud from one of the rooftops.

Suddenly he heard the sound of sirens. He looked down a found numerous police cars blasting through the streets as fast as they could. Nowhere near Sonic's speed though it was still quite fast for your average person. Sonic started to smile as he thought that this could be the beginning of a new adventure.

Sonic jumped off the roof and found his way to the ground safely. He dashed towards the police cars and followed them to a large courtyard.

In the Courtyard where groups of policemen firing guns at a strange creature. The bullets passed through him without even causing a scratch.

"Oh no our weapons are useless!'' One of the officers declared.

 **"All officers fall back!''** There superior officer announced with a megaphone.

The policemen ran as Sonic landed on the bonnet of one of the police cars.

"Hi there. Name's Sonic what's yours?"

The creature didn't answer. Instead all you could hear were some cries of "Oh my god is that really him? The legendary hero Sonic. He'll make quick work of this creature!"

"Not talking huh? Well maybe it's time you left. For some reason the people of this city don't like you. Best to just go and find somewhere else!''

The beast suddenly threw a punch with a stretched arm at Sonic. Sonic jumped out of the way and landed on the floor next to him.

"Oh so that's how you want to play. Ok then show me what you got,'' Sonic taunted the beast who tried another punch though Sonic dodged it quickly enough by jumping in a spin ball attack. He landed with the full force of his attack on the Beast's head. That brain thing was the only thing that looked like it could be a weak spot so that's where Sonic landed and sure enough the beast burst into loads of drops.

The drops soon formed a puddle and to Sonic's surprised reformed and quickly attacked with both arms stretched. His helicopter like attack smacked Sonic onto the floor.

"Lucky hit," The hedgehog responded as he avoided the Beast's next attack and jumped into the head again. It burst into drops again after wincing a little in pain. When it reformed this time the beast leaped high into the air onto the tops of the nearby flagpoles. Grabbing hold, the Beast smashed the floor with its fists. An attack Sonic easily dodged though the Beast leaped from pole to pole and kept striking the floor near Sonic.

Sonic decided enough was enough and spin dashed into the pole the Beast was about to land on. The Beast fell, crashing into the floor leaving him open for one final assault. This time the puddle didn't reform and retreated towards a drain.

"Hey you big drip. Where you going?"

The Beast disappeared down the drain.

"You know nothing you fool. That's Chaos the God of Destruction,",said a familiar voice.

It was Dr. Robotnik on top of the rooftops.

"Well well if it isn't Robotnik. I was wondering when you'd show up. So is this Chaos thing your latest weapon? How lame!"

"Confident as always you blue rat, but that was just the warm up. The real fight should be far more interesting. Until we meet again Hedgehog," Dr. Robotnik remarked before taking to the skies in his eggmobile.

After that Sonic found himself invited to stay in Emerald Resort Hotel by the Mayor himself. He even ran into Amy Rose who he had saved from the small planet. He decided to stay a few days in case that Chaos creature attacked again. Once in he checked in for the night and got a good night sleep.


	2. The Doctor's Plot!

The Chaos Users

0

Pairings Undecided

0

''Normal Speech''

 _Inner Thoughts, Dialogue, or reading passages from books and scrolls_

(Quick Notes and Messages or Echoes.)

 **(Dark over lapping echoes)**

 **''Boss Summons, Demons, Dark beings speaking, Demonic/Angry characters Speaking as well as extremely Dark spells and Magic.''**

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Story Start

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Above the clear blue skies a plane soared above. Tails was currently flying Sonic's plane, The Tornado, a red bi-plane that the hedgehog rarely used. The Blue Hero had left it in his possession since he loved to tinker with anything mechanical. So far all tests with a Chaos Emerald as a source of power was successful until the engine suddenly stopped. Tails tried to stop the plane from crashing but it was no use as the plane plummeted towards the ground. He gave a scream as he waited for the impact.

Everything had went dark after that.

* * *

In the Mystic Ruins Bonnie was in the forest, training her technique. The quiet and peaceful area proved rather serene and gave off the right atmosphere for training.

''Naruto…ah'm busy,'' Bunnie said as her lover massaged her sides. She found it kind of hard to focus when he insisted on being frisk.

''But Bun-nie,'' He said nibbling on her ear causing her to moan. ''I'm lonely,'' He said as his hand snake upward and started massaging her chest through her shirt. She was currently in her workout clothes, a tank top and yoga pants that did little to hide her athletic figure and shapely behind. He supposed she was working off her frustrations.

She worked as a hair dresser in Station Square to help pay for their apartment in the city.

''Ah…Naruto please, ah'm trying to practice mah technique…'' She said as she shivered at his touch.

''But I know a more fun way to work off that carrot cake I bought…'' He began trailing off as he got her attention.

''If you let me practice now ah promise we'll spend some quality time later okay?'' She said as Naruto kissed the back of her neck causing her to shiver again.

''Alright…you win…I'll be in the city…I'll be back in a few hours,'' The blonde said as he went outside the shop and made a bee-line for the train platform.

* * *

Knuckles had dug through into the ground in pursuit of the liquid creature that shattered the Master Emerald. He eventually emerged from the ground poking his head through. He found himself in the city, and as he looked around he saw a sign that said 'Station Square.''

* * *

"Sonic!" Naruto cried out in surprise as he was about to board the train. "And you as well Tails?"

"Hey Naruto!" Tails waved;

"Been a while. How's Bonnie?"

"She's good. Kicked me out of our training spot so I have nothing to do. So what are you guys up to?"

"I was just about to show Sonic something at my workshop. Want to come?"

"Sure I have nothing better to do." The trip to Tail's shop wasn't that long.

"Cool Workshop Tails," Sonic called out as they reached the top of the stone steps.

Suddenly the sound of Jet engines interrupted their short would be conversation. Above them flew the Doctor in his Eggmobile. This time it had two stumpy wings with a massive spike on each. The Doctor descended onto the flat platform.

"Hey look it's a giant talking Egg," Sonic pointed out with his characteristic smile.

"What are you doing here? Didn't you get enough of a beating last time?" Tails taunted him.

"Silence! I the great Dr Ivo Robotnik will soon be the ruler of this planet. You have a Chaos Emerald, give it to me or prepare to face the power of my Egg Hornet!"

"Not a chance. Bring it on Eggman!"

The Egg Hornet's engine roared and attacked Sonic, who had been itching to fight the Doctor again.

Sonic jumped out of the way as Tails attacked the cockpit glass. Annoyed Dr. Robotnik switched his focus from Sonic to Tails which left him open to Sonic's attacks. He flew into and shot out several missiles. This time Naruto shot forward and sent the missiles flying from the force of his punches.

Sonic followed up with the Homing attack to destroying one rocket launchers while Tails use his tails to slice the other half. No matter what the doctor tried it was a losing situation.

 _''That was too easy even for Robotnik."_

Robotnik didn't seem to move; instead he pretended to smash the controls of his ship with his fist. As Tails ran towards Sonic he noticed the glimmer of the Emerald. He knew the troublesome fox had one of the seven chaos emeralds and now was the time to strike.

A huge claw came out of nowhere and snatched the Chaos Emerald from Tails' grasp. The Claw brought the Emerald into the Doctors grasp.

"Thank you twerp. One seventh of my plan is now complete. Oh Chaos!" Dr. Robotnik called out.

A puddle of water appeared out of nowhere, morphing into the same beast Sonic fought outside Station Square's City Hall.

''Chaos!'' Naruto shouted surprising everyone. Somehow the blonde knew about the liquid creature.

''You know this creature Naruto?'' Sonic asked with a raised eye.

''Yeah and at all costs he must never acquire all seven emeralds,'' Naruto said as he clenched his hand. _''I won't let the world almost be destroyed again Tikal,''_ He whispered but Sonic and Tails still heard him.

''Aah well then boy you know that once Chaos has reached its perfect form I will rule the world and Robotropolis will be built at last.''

The Doctor threw the emerald at Chaos and it disappeared into its body. Chaos melted back into a puddle and reformed only this time he was slightly different. A strange stone like bone appeared in one of his arms. Chaos 1 whipped his arm as the tendril like appendages expended. Naruto dashed in front of Tails to take the brunt of the hit as the two of them were sent flying down the staircase.

''NARUTO! TAILS! Eggman you bastard! You'll pay for that!'' Sonic said as he ran forward.

Chaos wasn't fast enough to move in front of the doctor so instead he mashed the ground as wind seemed to cut up the ground tossing up several rocks eschewing Sonic's path causing him stop. ' _The hell! Was it that creature Chaos? Or was it the Chaos Emerald that did that?'_

"As you can see Chaos gets stronger with every emerald he absorbs. When he gets all seven he'll be invincible and that's when I strike!''

"That thing is nothing but a big drip. I stopped it once I can stop it again!''

Sonic raced over to fight Chaos though the liquid life form just melted into a puddle again and disappeared into the ground.

"Not here Rodent. We will meet again though and next time we will be ready for you." And with that Dr. Robotnik took to the skies.

Sonic paused to think. "He needs more emeralds to power Chaos."

''Meaning we beat the bastard to the punch.'' Naruto said as he and Tails made it back to the top. ''I know where there's another Chaos Emerald.''

* * *

Meanwhile back in Station Square Knuckles had arrived to find he could not find the liquid life form.

It was the first time Knuckles had left his island and entered a big city in the human world. Deciding that the creature meant nothing at the moment as restoring the Master Emerald and Angel Island was his top priority. He focused and meditated sensing the shards of the emeralds over the plane. He could sense a few were back in the Mystic Ruins but he could get those later. Right now the ones in the city were top priority as there was a good chance they could be taken for jewels.

It didn't take long for Knuckles to find the three shards as he searched the city. One was inside a building, another in a tree and the last one was under a bell. So far three pieces of the shattered emerald had been found so now it was time to turn his attention to the next closet signal.

* * *

Amy Rose happily hummed as she made her way through the city. She had adapted herself quite well to living in Station Square. She glanced over at her Piko Piko Hammer, her weapon of choice to fight off Eggman's machines. She figured that the reason Sonic didn't display much attention in her because she simply wasn't a fighter. Maybe if she could prove herself capable then her hero would profess his everlasting love for her. She squealed at the moment as more romantic images flooding her mind. She knew ever sense her Fortunetelling cards foretold a blue hero saving her from a small planet it was destiny.

Though love would have to wait at the moment as she would have to go buy some groceries seeing as she was currently low on food.

In another Part of the City Big the Cat had followed his frog friend all the way to the big city. He didn't care much for cities, too busy and hectic for him. He spotted Froggy hopping around the streets and watched as he hopped under a car and down a drain. Big lifted the car and fell through the drain into the sewers.

Big followed Froggy into Twinkle Park the big amusement park of Station Square. It sat on the coastline of Station Square and was very popular with children. Big had gotten through using the maintenance tunnels and found himself in front of a big pool. Big examined the pool and found it full of fish, amongst which was Froggy swimming.

Big wasn't too fond of swimming but he was very fond of Fishing. He took out his Fishing Rod and launched his lure into the water near Froggy.

Just like a fish Froggy fell for the lure and Big snagged him. It wasn't easy to reel him in, but Big managed it, finally catching his best friend.

"Froggy? Why are you running away from me? What has gotten into you?" asked Big.

Froggy sneered at Big and started to fidget. Something was definitely wrong with Froggy; it was as if he was trying to find something. Big took Froggy out of Twinkle Park quickly and avoided the security. Lucky for him he was quick enough to catch Froggy and get out before anyone noticed him.

Victorious Big headed back to his little hut in Mystic Ruins.

* * *

Naruto blasted through the Mystic Ruins Windy valley as his three companions followed close behind him. Once told that Robotnik was back to his old tricks Bonnie was happy to tag along and help any way she could.

As they blazed through the path they were eventually picked up by a Tornado. Because of his strong affinity for wind Naruto was able to control the elemental disaster and used it to quickly comb through the area until they found the Blue Chaos Emerald.

"Excellent. One down, five to go!'' Sonic declared.

"Ya know ah think ah remember readin' about an emerald locked in a vault in the casino in town." Bonnie spoke up, relaying the information he read in the paper the other day.

"Its own Emerald?" Sonic questioned her.

"The Mayor bought it from an archaeologist to put in a museum. Though they feared for its safety so they placed it in the Casino area's vault, which has never been broken into in its history.''

"Well there's a first time for everything. Come on let's go!''

After forming a hole through the door of the vault of Casionopolis Naruto got the Silver Chaos Emerald.

 _''Two down all we need is four more,''_ Naruto began to ponder where they could go now that they exhausted their leads?

''So where do you think…'' Tails started to ask before being interrupted by a cloud of Purple smoke.

"Ho Ho! Thanks for getting the Emerald from me. Night Night you pests", Dr. Robotnik called out as he flew away.

"Damn!" Sonic grunted before falling asleep

"Egg….man" Tails before he fell asleep.

''Damn...not here...'' Naruto said as he struggled against the effects of the gas. He was able to stay awake, but he was so sluggish that the only thing he could do was wait for a few minutes as the compound burned out of his system.

* * *

Knuckles decided to take in the sights of the city for now as when he got to the Casino it was closed. He had to wait until Nightfall as the casino only opened at night. He was really impressed by the city. Amazed by the friendliness of its people and the incredibly tall buildings.

When night came he headed straight for the Casino. Though as he left the hotel to get to the Casino area he came across a familiar foe.

There entering an elevator was Dr. Robotnik, the reason Angel Island fell from the Sky the first time and Knuckles started to think he was behind it this time. He followed Dr. Robotnik by noting the floor the doctor got off at and entered the same elevator.

As the doors opened he saw Dr. Robotnik just standing there in the middle of an empty room. It was some kind of ballroom probably used to host big events.

"Ok doctor put em up. What are you doing here? What are you up to?" Knuckles demanded from the human.

The Doctor turned and was surprised to see Knuckles preparing his fists.

"Kn…Knuckles? What are you doing here? Shouldn't you be looking for those Master Emerald shards?" Dr. Robotnik asked, genuinely surprised that the Enchinda was there.

"What? How did you know about that? I knew you were behind it" Knuckles angrily accused him.

The doctor started to panic and slowly walk backwards. A Giant puddle appeared on the floor.

"Ah Chaos. I was wondering where you got to! HERE!" Dr. Robotnik shouted throwing the grey Chaos Emerald towards the puddle.

The puddle absorbed the Chaos Emerald and reformed as Chaos 2. The head seemed to grow some sort of stumpy bull horns and each arm was reinforced with two stone like bones.

"You! I was wondering where you got to! Right that it's, this time I'm not letting you get away."

"Chaos... attack!"


	3. Knuckles Enters the Fray!

The Chaos Users

0

Pairings Undecided

0

''Normal Speech''

 _Inner Thoughts, Dialogue, or reading passages from books and scrolls_

(Quick Notes and Messages or Echoes.)

 **(Dark over lapping echoes)**

 **''Boss Summons, Demons, Dark beings speaking, Demonic/Angry characters Speaking as well as extremely Dark spells and Magic.''**

0000000000

Story Start

00000

Chaos's new form sported two arms that were now larger and have emeralds in both of them. Its head has moved forward, giving it a more unpleasant appearance, the horns on his head have also changed position to give it a hammerhead style look.

 **''It may be only two emeralds but it'll be more than enough to defeat you Echinda,''** Chaos announced shocking both Occupants.

''C-C-C-Chaos! You can talk?'' Robotnik stammered out in shock. He had no idea that the being's sentience extended that far.

 **''It was arrogant to assume I was just some mindless beast. Now to pick up where I left off.''**

''It doesn't matter speech or no speech you're going to pay for smashing the emerald,'' Knuckles said as he dashed forward and punched.

Reacting quickly Chaos created a large shield of water that halted the Enchinda's attack.

 **''Fool…did you think such a simple attack could work on me?''** Chaos remarked as he brought up his hands and smashed them to the ground causing shock-waves. Knuckles jumped into the air and glided to the other side of the room to avoid it. He then charged forward again throwing both fist but Chaos changed itself into a massive ball of water and dodged it.

The liquid creature bounced across the room destroying chairs and table as it left moisture on the ground. Knuckles started to play on the defense as he back flipped and side stepped the initial attacks waited for the right moment. He then charged and released a brutal dash punched that sent Chaos flying backwards smashing into a pillar. Chaos collapsed into a puddle. Chaos then reformed itself. **''You're stronger than the others of your kind, I will give you that, but now the games are over,''** Chaos said as it dispersed into a massive amount of water and created a giant sphere around Knuckles.

The Enchinda tried to punch through the walls of the creature but it was futile. Chaos constricted into a smaller sphere attempted to drown the enchinda as there was only so long he could hold his breath.

 _'Damn I can't give up…must focus…I got to…I can't!''_ Knuckles thought as he started to lose consciousness.

 _Do not give up…_ A voice said as Knuckles found himself in darkness.

''Hello…where am I? Whose there?''

 _You have much power within you…The holy guardian of the master emerald…you have an inner fire within you that can't be distinguished…fight on._ The voice said as it vanished.

Knuckles eyes widen as he looked around. He began to focus and reached deep inside of himself. His body started to heated to extreme temperatures. _Let's see how you like this …My Maximum Heat Attack._ Knuckles thought as he released a series of punches while blasted out fire burning and ripping Chaos 2 apart.

Chaos returned to his portal form as to circular lights which one would only assume were the Chaos Emerald floated above him.

 **''You win this time Echina but I'll be back,''** The liquid creature said as he slipped through the cracks in the floor.

The Doctor began to panic.

"Easy now Knuckles. I'm not who you're after remember,'' The Doctor spoke up, hoping to pull a fast one on the guardians.

"Can it Eggman. You are in cahoots with that monster Chaos and he appeared shortly after the Master Emerald shattered. I know you have something to do with it!" The Enchinda declared angrily as he poised to attack.

Dr. Robotnik smiled. "Don't see you're on a wild goose chase…Sonic and his friends are the ones you're after.''

"Sonic and the others? What do they have to do with anything?"

"I hear they are collecting Master Emerald Shards."

"What? Why would they…? How would they….? This doesn't make any sense", said Knuckles.

''Chaos grows stronger from Chaos Emeralds, not the Master Emerald. What need would I have for it?'' The Doctor asked playing on Knuckles naive like nature.

He made a good point. Eggman gave Chaos the Silver Emerald and he didn't sense any of the Master Emerald shards near the doctor and reluctantly turned his back on the Doctor.

"Don't think I'm just going to let you do what you wish. I'll be back for you and Chaos later." Knuckles warned him before leaving the room.

Knuckles returned to his quest to find the Master Emerald shards and headed straight for the Casino.

Knuckles felt a signal and immediately left them to pursue it. Inside the Casino he was blinded by bright neon lights and his feet were on fire. Somewhere inside the building there were Emerald shards and he was going to find them.

Knuckles felt the first signal emanating from the giant Sonic statue in front of him.

After smashing the statue into pieces and taking the Emerald shard from inside it.

He quickly found the other two shards and the trio were gone when he exited the trio. Knuckles found himself surrounded by a strange orb and blacked out.

When he came too he found himself in front of a temple. ''Where in the world am I?'' He said looking around some more. ''This place feels familiar…He looked around and was astonished by the sight but what was shocking he came across two other Enchinda.''

''Father! Please Don't!'' The speaker was a young female enchinda with light orange fur. She wore a tanktop-like garment which revealed her midriff and the traditional tribal dress with beige, green, and red triangular patterns. As a sign of her lineage, she wore a golden necklace and tiara-like band atop her forehead, both of which were decorated with a blue jewel in the center. Her white gloves were adorned with thick, cobalt-blue bracelets around her wrists, and she wore white-strapped sandals. Her dreadlocks were also wrapped with similar white bandages.

She was speaking to a dark red-violet male. One much older with tribal get up as well. His consisted of green, red, and dark brown colors with a collar and in his hand he carried a sphere with the metal being some strange sort of cobalt blue substance. Unlike the girl his dreadlocks hung in the back and there were four fine orange line patches running through the top of his head.

''Tikal the seven emeralds are essential to our survival. It is for the good of our people!'' the male remained stubborn and form in his beliefs.

''How can I make you understand…Attacking our countries…stealing and killing…it's wrong…It can't be the path to peace…no one has the right to take their holy ground…I beg of you father!'' The girl pleaded to him with no avail.

It was over as soon as it happened and Knuckles found himself back in station square.

The quartet had awoken angry that they were poisoned like that. They still luckily had one emerald and thank god Robotnik was far too stupid to consider putting a bullet in their skulls when they were incapacitated.

They were already making their way to the Mystic Ruins area when a loud explosion occur, causing a slight tremor.

Nothing good could come from the sound as it was an explosion. As if someone blasted into the mountain with a large cannon.

''The emerald is reacting…I think the next emerald is through that hole in the mountain,'' Naruto pointed out so they continued on, finally arriving to the site of the destruction.

"Where are we?" Bunnie asked, as they traveled through the caverns before arriving to the winter wonderlands of Angel Island.

"There is no mistaking it. This is the Icy regions of Angel Island." Sonic pointed out, it had been quite some time since he had been on the island.

"It was around this time we met I believe." Naruto noted, pursing his lips. He couldn't help but remember just how he had been tricked when he first arrived in this world. "Anyway the emerald is reacting, no time to reminiscence lets go." Naruto remarked.

As they tread down the icy cascades of the winter wonderland they saw evidence that even more of the world was effected by the chaos cross event then they realized. Parts of this world now resembled parts of the worlds in Mobius and was dubbed with the same names in Mobius.

It didn't take long for them to snow board down the mountain and find the other green emerald.

With four down that left only three of them.

Not to mention they even found a few Master Emerald Shards. Meaning sooner or later Knuckles would show up. ''Now that were out of place you can shed those clothes,'' He said winking suggestively and speaking of Bunnie's snow gear.

She rolled her eyes and got to doing so since it was getting pretty hot. She shed the snow pants and jacket while adjusting her shirt. ''Is that better?'' She asked him dryly.

''I think a few more articles…'' He began until Sonic interrupted him.

''Yo love birds we have a job too do…I don't think making kits or cabbits or whatever will be beneficial don't you think?'' Sonic asked teasing them as Naruto rolled his eyes and Bunnie blushed.

"You're just jealous she likes me now." Naruto teased in turn.

Sonic shook his head. ''Anyway the Emerald is reacting towards the water fall…looks like we have another emerald to get,'' Sonic said as he tossed the green emerald up into the air and caught it.

''Hey isn't that...'' Tails called out, seeing something red in the distance.

Coincidentally at that time Knuckles had arrived in the Mystic Ruins again. His search for the emeralds were halting when he saw a green glow in Sonic's hand…Naruto walked over with a similar looking glow and his senses set off saying that Master Emerald shards were down there.

 _'No it couldn't be. Eggman was right that's a Master Emerald shard.'_

Knuckles raced over to the trio and roared out the Blue Hedgehog's name. They jumped to face Knuckles taking a fighting stance. Knuckles was angry, that was obvious, and at them, what had they done?

''Give me all the emeralds you have right now!'' The Enchina demanded.

''Settle down Knucklhead! We need the emeralds. ''

"Calm down Knuckles I can understand that you're after the shards, but we need the emeralds." Naruto's attempt to try and reason with the Enchinda failed when he misinterpreted Naruto's words.

"Nothing will stop me restoring the Master Emerald. Take this!" Knuckles shouted before throwing a series of high speed punches at the groups.

They immediately dodged as the grass was shredded as well as several trees nearby was uprooted.

Sonic jumped out of the way and used his spin attack on Knuckles. Knuckles dodged Sonic's attack but ignored Tails who grabbed hold of Naruto and flew into the air.

Bunnie leap up and kneed the Enchina in the stomach. Tails let go as Naruto spun and was about to kick the Enchinda when Knuckles suddenly spun and kicked Naruto in the face.

Bunnie using her leg strength launched at Knuckles, but her punch was easily neutralized as Knuckles used his arms to tank the hit.

Instantly he countered with two fierce body blows and a fiery uppercut that ripped part of her top and burned her. Bunnie let out a cry as she crashed into the side of one of the cabin's causing part of the wall to cave in.

Sonic was pissed but it was nothing compared to Naruto who shot like a bullet and hit Knuckles with a series of punches like a blur before the final hit sent him crashing through the mountain wall.

Knuckles dislodged himself from the wall. He charged at Naruto who was about to meet him halfway when suddenly a powerful beam landed on the ground, detonating and blasting all of them off their feet.

The two emeralds they had gathered fell to the ground. The area was littered with smoke and debris as the area by the water fall had been massively damaged by the unforeseen attack.

Nothing but ringing was in Naruto's ears as he looked around. His blurred vision could just make out the form of the emerald. Before Naruto could grab them one of Chaos' hands erupted from the ground.

The Doctor floated down from above as the canon from the eggmobile was just cooling down from the beam it used.

"Ha Ha! You fools brought two more emeralds to me. Time to feed Chaos."

"Wait Chaos Emeralds as well? That's what you were talking about when you said you needed the emeralds! What have I done?"

"You fool. You are so easily tricked. They weren't gathering the Master Emerald shards," Dr. Robotnik declared with a jovial laugh.

"He tricked you again! How could you fall for it twice?" Sonic couldn't believe Knuckles would trust Eggman after the first time he was lied to.

 **''I remember you…that energy…the one who helped sealed me before… ''** Chaos hissed angrily.

''Chaos, I know you're angry, but you got to stop before its too late. Tikal wouldn't…" he tried to reason with the monster to no avail.

 **''She failed! And so will you. This time things will end differently…with the Master Emerald shattered it's not here to save you now,''** He said swiping the emeralds from the Doctor's hand. **''Finally human, I was beginning to think I would have to go and find the remaining emeralds on my own.''** Chaos said much to Robotnik's annoyance.

Chaos swallowed the two chaos emeralds as a bright intense light enveloped them.

When the light faded all that remained was a shark like creature made out of water. More stone like bones appeared within the water beast, some clearly holding the emeralds in place.

Chaos dived into the Lake and swam in the water beneath the surface of the lake.

"I may have been tricked again but I won't let you get away with this!" Knuckles shouted.

"That's more like it. No way Chaos can stand all five of us."

''You ready Bunnie?'' Naruto asked.

''Any time…'' She said as they followed after them.

The five fighters had landed on giant floating lily pads.

The water seemed thicker, as Chaos had merged himself with the lake. As such any assault simply bounced of the surface of the water, yet if they landed in it they would start to sink, a bit like quicksand.

Chaos fired many attacks towards them from blasts of waters to waves. Despite his stronger form Chaos was a sitting duck. Naruto would duck his hand into the water heating it causing Chaos to shoot out of the water violently. Whenever he emerged Sonic, Tails, Bunnie or Knuckles was ready to strike his core. It was one thing to fight one opponent or maybe even two but five was too much for even Chaos himself in his current form.

Chaos roared in pain and left the arena. Before it left however it seemed to freeze, taking a good look at Knuckles. As if it was remembering something.

Meanwhile Dr. Robotnik had left the arena and above them was a huge flying battleship with his trademark logo.

''Behold my master piece, The Egg Carrier. You may have won this round heroes but once I gain the last three Emeralds none of you will stand a chance against Chaos and

with my Egg Carrier I will find them before you do", Dr. Robotnik said as he was pulled into the flying craft by a green tractor beam.

''Damn! He's not getting away…Tails the Tornado is still your workshop right?''

''Yeah the renovations have already been made.''

''What are we waiting for? Let's go,'' Naruto

"You guys go. I'm Sorry. I thought you were collecting the Master Emerald shards on you and when I saw the green light…" said Knuckles.

''Wait…'' Naruto stopped and tossed Knuckles the Emerald shards he found. ''I happened to find some…next time don't believe anything Eggman says and were good…ok team let's head out,'' He said as the three of them headed to the Workshop.

The Tornado's engines roared as it came so life taking off into the blue skies.

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Chapter End

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1\. I always thought it was retarded that Knuckles could sense Emerald shards but couldn't tell at this moment that was a Chaos Emerald Sonic had…now I made it plausible…oh and I'm obviously using some of the UK comic plot devices for Chaos.


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